ViewGene
Locus Name:
GeneID:
Location:

GeneID:4221
TrivialName: PA14_09000
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_09000
PAO1 Ortholog Locus:PA4248
Sequence Length:534
Protein Length:177
Start: 766351
Stop: 766884
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07636.1|AE004841_14 (AE004841) 50S ribosomal protein L6 [Pseudomonas aeruginosa PAO1]
Identities = 177/177 (100%), Positives = 177/177 (100%)
Sequence:
ATGTCTCGCGTTGCTAAGAACCCCGTCAAGCTGCCTGCCGGCGTTGAAATCAAACTGGCTGGTCAGCAACTG
TCCATCAAGGGCGCCAAAGGTGCTCTGGAGCTCAAGGTCCATCCTTCGGTCGAAGTGATCCAGGACAGCGGT
GAGCTGCGTTTTGCTGCGCGTAACGGCGACCAGCAGACTCGCGCCATGGCTGGTACCACCCGTGCTCTGGTG
AACAACATGGTAGTCGGCGTCAGCCAGGGCTTCGAGCGCAAGCTCCAGCTGGTCGGCGTTGGTTACAAAGCG
CAGGCCAAGGGCCAAGTGCTGTCCCTGTCCCTCGGCTTCTCCCATCCGGTTGATTACGAACTGCCGGCCGGC
ATCGTCGCTGAGACCCCCAGCCAGACCGATATCCTGATCAAGGGTATCGACAAGCAGCTGGTCGGTCAGGTT
GCTGCCGAAATTCGCGACTTCCGTCCGCCGGAGCCTTACAAAGGCAAGGGCGTGCGTTACGCCGACGAAGTC
GTCCGTCGTAAAGAAGCCAAGAAGAAGTAG
Translation:
MSRVAKNPVKLPAGVEIKLAGQQLSIKGAKGALELKVHPSVEVIQDSGELRFAARNGDQQTRAMAGTTRALV
NNMVVGVSQGFERKLQLVGVGYKAQAKGQVLSLSLGFSHPVDYELPAGIVAETPSQTDILIKGIDKQLVGQV
AAEIRDFRPPEPYKGKGVRYADEVVRRKEAKKK*
AnnotationID:4227GeneID:4221
AnnotatorUID: diggins
Modification Date/Time: 2005-04-03 09:09:36
Gene Name:rplF
Confidence Code:2
GeneProduct:50S ribosomal protein L6
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(26) Translation, post-translational modification, degradation
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0097,pfam00347
Secondary Functional Category(ies):translation, ribosomal structure and biogenesis
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN66099.1|AE016238_17 (AE016775) ribosomal protein L6 [Pseudomonas putida KT2440]
          Length = 177

 Score =  317 bits (811), Expect = 3e-86
 Identities = 160/177 (90%), Positives = 167/177 (94%)

>gb|AAO54183.1| (AE016858) ribosomal protein L6 [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 177

 Score =  311 bits (798), Expect = 9e-85
 Identities = 156/177 (88%), Positives = 168/177 (94%)

>gb|AAM87548.1|AE014003_6 (AE014003) 50S ribosomal subunit protein L6 [Yersinia pestis KIM]
          Length = 177

 Score =  236 bits (601), Expect = 6e-62
 Identities = 118/177 (66%), Positives = 143/177 (80%)






 
Structural Features:
COG0097, RplF, Ribosomal protein L6P/L9E 
[Translation, ribosomal structure and biogenesis]
CD-Length = 178 residues,  98.9% aligned
Score =  221 bits (564), Expect = 5e-59
Identities = 90/176 (51%), Positives = 122/176 (69%)

pfam00347, Ribosomal_L6, Ribosomal protein L6.
CD-Length = 77 residues,  98.7% aligned
Score = 74.5 bits (183), Expect = 7e-15
Identities = 31/76 (40%), Positives = 44/76 (57%), Gaps = 1/76 (1%)







   
Genomic Context:






   
Comment:


















    ReferenceID:8444




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:25585




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36533




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:4221_cdd.html


    		




 
URL:

















    ReferenceID:36723




  
Author/Investigator(s):
        Cerretti DP, Dean D, Davis GR, Bedwell DM, Nomura M.





  
Title:
        The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene.




  
PubMed:
        6222285


MedLine:
        




    
Source:
Nucleic Acids Res. 1983 May 11;11(9):2599-616.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=6222285

















    ReferenceID:36729




  
Author/Investigator(s):
        Davies C, Bussiere DE, Golden BL, Porter SJ, Ramakrishnan V, White SW.





  
Title:
        Ribosomal proteins S5 and L6: high-resolution crystal structures and roles in protein synthesis and antibiotic resistance.




  
PubMed:
        9642068


MedLine:
        




    
Source:
J Mol Biol. 1998 Jun 19;279(4):873-88.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=98307993&dopt=Abstract

















    ReferenceID:36752




  
Author/Investigator(s):
        Chen R, Arfsten U, Chen-Schmeisser U.





  
Title:
        The primary structure of protein L6 from the aminoacyl-tRNA binding site of the Escherichia coli ribosome.




  
PubMed:
        324885


MedLine:
        




    
Source:
Hoppe Seylers Z Physiol Chem. 1977 Apr;358(4):531-5.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=77186588&dopt=Abstract









           
Homologs By Global Alignment 

           

       



     
Gene ID:4221
           
Identity:

                               
                                   0%
                               
                                   10%
                               
                                   20%
                               
                                   30%
                               
                                   40%
                               
                                   50%
                               
                                   60%
                               
                                   70%
                               
                                   80%
                               
                                   90%
                               
                                   100%
                               
                             

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6507
                           PA4248_tr
                           translation of PA4248
                           177
                           99.99
                           99.99
                           0
                           880.0
     

     
     
176830
                           gb|AAG07636.1|AE004841_14
                           (AE004841) 50S ribosomal protein L6 [Pseudomonas aeruginosa PAO1]
                           177
                           99.99
                           99.99
                           0
                           880.0
     

     
     
176831
                           gb|AAN66099.1|AE016238_17
                           (AE016775) ribosomal protein L6 [Pseudomonas putida KT2440]
                           177
                           90.39
                           94.35
                           0
                           811.0
     

     
     
176832
                           gb|AAO54183.1|
                           (AE016858) ribosomal protein L6 [Pseudomonas syringae pv. tomato str. DC3000]
                           177
                           88.13
                           94.91
                           0
                           798.0
     

     
     
176834
                           gb|AAQ61831.1|
                           (AE016924) 50S ribosomal protein L6 [Chromobacterium violaceum ATCC 12472]
                           177
                           67.23
                           81.35
                           0
                           602.0
     

     






      

          
GC ORFID: 47223How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4248Glimmer Score: 

          
Start: 4187588Stop: 4187055

          
Length: 534


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAGTruncated Stop: 

          
Homolog: t_PA4248 translation of PA4248Homolog Bit Score 343.0

          
Other Homologs:  psyr_15may02_Scaffold4_revised_gene5200 (ORF: BLASTX 307.0), t_PA4248 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCTCGCGTTGCTAAGAACCCCGTCAAGCTGCCTGCCGGCGTTGAAATCAAACTGGCTGGTCAGCAACTG 
TCCATCAAGGGCGCCAAAGGTGCTCTGGAGCTCAAGGTCCATCCTTCGGTCGAAGTGATCCAGGACAGCGGT 
GAGCTGCGTTTTGCTGCGCGTAACGGCGACCAGCAGACTCGCGCCATGGCTGGTACCACCCGTGCTCTGGTG 
AACAACATGGTAGTCGGCGTCAGCCAGGGCTTCGAGCGCAAGCTCCAGCTGGTCGGCGTTGGTTACAAAGCG 
CAGGCCAAGGGCCAAGTGCTGTCCCTGTCCCTCGGCTTCTCCCATCCGGTTGATTACGAACTGCCGGCCGGC 
ATCGTCGCTGAGACCCCCAGCCAGACCGATATCCTGATCAAGGGTATCGACAAGCAGCTGGTCGGTCAGGTT 
GCTGCCGAAATTCGCGACTTCCGTCCGCCGGAGCCTTACAAAGGCAAGGGCGTGCGTTACGCCGACGAAGTC 
GTCCGTCGTAAAGAAGCCAAGAAGAAGTAG